--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/methylGSA.R	Thu May 20 08:44:37 2021 +0000
@@ -0,0 +1,79 @@
+###############################################################################
+# title: MethylGSA
+# author: Xiaowei
+# time: Mar.31 2021
+###############################################################################
+
+spec <- matrix(c("data_file", "D",1, "character", "txt file",
+                 "test_method","M",1,"character", "Test method",
+                 "array_type","T",1,"character","Array type, 450K, EPCI",
+                 "group","G",1,"character","group: all, body, promoter1, promoter2",
+                 "GS_list","L",1,"character","Gene Set tested: Gene Ontology, KEGG, Reactome",
+                 "minsize","I",1,"integer", "Minimum gene set size",
+                 "maxsize","A",1,"integer", "Maximum gene set size",
+                 "result", "R", 1, "character", "result table"
+                 ), byrow = TRUE, ncol = 5)
+
+opt <- getopt::getopt(spec)
+
+
+# #===========================================================================
+# #输入的参数
+# #===========================================================================
+# # txt文件
+# opt$data_file
+# opt$test_method
+# opt$array_type
+# opt$group
+# opt$GS_list
+# opt$minsize
+# opt$maxsize
+
+
+temp = read.table(opt$data_file)
+cpg.pval1 = temp[,2]
+names(cpg.pval1) = temp[,1]
+inputmethod = opt$test_method
+
+#================================================================
+#run codes
+#================================================================
+suppressPackageStartupMessages(library(methylGSA))
+
+
+if(opt$array_type=="450K"){
+  suppressMessages(library(IlluminaHumanMethylation450kanno.ilmn12.hg19))
+}else{
+  suppressMessages(library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19))
+}
+
+if(inputmethod == "methylglm"){
+  res <- methylglm(cpg.pval = cpg.pval1, array.type = opt$array_type,
+              group = opt$group, GS.list=NULL, 
+              GS.idtype = "SYMBOL", GS.type = opt$GS_list, 
+              minsize = opt$minsize, maxsize = opt$maxsize)
+
+}
+
+if(inputmethod == "RRA_ORA"){
+  res <- methylRRA(cpg.pval = cpg.pval1, array.type = opt$array_type, 
+              group = opt$group, method = "ORA", 
+              GS.list=NULL, GS.idtype = "SYMBOL", GS.type = opt$GS_list, 
+              minsize = opt$minsize, maxsize = opt$maxsize)
+}
+
+if(inputmethod == "RRA_GSEA"){
+  res <- methylRRA(cpg.pval = cpg.pval1, array.type = opt$array_type, 
+              group = opt$group, method = "GSEA", 
+              GS.list=NULL, GS.idtype = "SYMBOL", GS.type = opt$GS_list, 
+              minsize = opt$minsize, maxsize = opt$maxsize)
+}
+
+if(inputmethod == "gometh"){
+  res <- methylgometh(cpg.pval = cpg.pval1, sig.cut = 0.001, array.type = opt$array_type, 
+                 GS.list=NULL, GS.idtype = "SYMBOL", GS.type = opt$GS_list, 
+                 minsize = opt$minsize, maxsize = opt$maxsize)
+}
+
+#===============================================================================
+write.csv(res, file = opt$result)